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mmu_circItch_598
Basic information of circular RNA
PanCircBase ID:
mmu_circItch_598
mm39_Chr. Position ID:
chr2|155051906|155060007|+
Gene name:
Itch
Transcript:
ENSMUST00000029126.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
19,20,21,22,23
Exon/intron offsets:
0,453,2350,3011,8004
Genomic length:
8101
Exon/intron sizes in nt:
134,141,121,105,97
Flanking exon/introns:
chr2:155051138-155051906|chr2:155060007-155062127
Splice length:
598
Other database IDs:
circAtlas: mmu-Itch_0041
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_356383
Human Ortholog IDs:
Mature spliced Sequence:
GCTCTGTTTCATGGGAAATTCATAGATACCGGATTTTCTTTACCATTCTATAAACGTATCCTGAATAAACCAGTTGGACTGAAGGATTTAGAATCTATTGATCCAGAATTTTATAATTCGCTCATCTGGGTTAAAGAAAACAACATTGAAGAATGTGGTTTGGAAATGTACTTCTCAGTTGATAAAGAAATTCTAGGTGAAATTAAGAGTCATGATTTGAAACCCAATGGTGGCAATATTCTTGTGACAGAAGAAAACAAGGAGGAATACATCAGGATGGTAGCTGAGTGGAGGTTGTCTCGAGGTGTTGAAGAACAGACACAAGCTTTCTTTGAGGGCTTTAATGAAATTCTTCCTCAGCAATATTTGCAATATTTTGATGCGAAGGAATTAGAGGTTCTTCTGTGTGGGATGCAGGAGATTGATTTGAATGACTGGCAGAGACATGCCATCTACCGCCACTACACCAGAACAAGCAAGCAGATCATGTGGTTTTGGCAGTTTGTTAAAGAAATTGATAATGAGAAGAGGATGAGACTTCTGCAGTTTGTTACTGGAACCTGCCGATTGCCAGTGGGAGGATTTGCTGACCTTATGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTTACTGGAACCTGCCGA
59.24
AAATCCTTCAGTCCAACTGGT
57.12
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTGTTACTGGAACCTGCCGA
59.86
AATCCTTCAGTCCAACTGGT
56.35
140
PCR template sequence:
CAGTTTGTTAAAGAAATTGATAATGAGAAGAGGATGAGACTTCTGCAGTTTGTTACTGGAACCTGCCGATTGCCAGTGGGAGGATTTGCTGACCTTATGGGCTCTGTTTCATGGGAAATTCATAGATACCGGATTTTCTTTACCATTCTATAAACGTATCCTGAATAAACCAGTTGGACTGAAGGATTTAGAATCTATTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-802-5p(1), mmu-miR-377-3p(1), mmu-miR-5101(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTGACCTTATGGGCTCTGTTTCATG
siRNA sets
TGAAACAGAGCCCATAAGG, AACAGAGCCCATAAGGTCA, ATGAAACAGAGCCCATAAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCITCH_598_ORF_1
0.8249
0.110853394
0.55559543
486
ORF sequence:
ATGTACTTCTCAGTTGATAAAGAAATTCTAGGTGAAATTAAGAGTCATGATTTGAAACCCAATGGTGGCAATATTCTTGTGACAGAAGAAAACAAGGAGGAATACATCAGGATGGTAGCTGAGTGGAGGTTGTCTCGAGGTGTTGAAGAACAGACACAAGCTTTCTTTGAGGGCTTTAATGAAATTCTTCCTCAGCAATATTTGCAATATTTTGATGCGAAGGAATTAGAGGTTCTTCTGTGTGGGATGCAGGAGATTGATTTGAATGACTGGCAGAGACATGCCATCTACCGCCACTACACCAGAACAAGCAAGCAGATCATGTGGTTTTGGCAGTTTGTTAAAGAAATTGATAATGAGAAGAGGATGAGACTTCTGCAGTTTGTTACTGGAACCTGCCGATTGCCAGTGGGAGGATTTGCTGACCTTATGGGCTCTGTTTCATGGGAAATTCATAGATACCGGATTTTCTTTACCATTCTATAA
Peptide sequence:
MYFSVDKEILGEIKSHDLKPNGGNILVTEENKEEYIRMVAEWRLSRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCGMQEIDLNDWQRHAIYRHYTRTSKQIMWFWQFVKEIDNEKRMRLLQFVTGTCRLPVGGFADLMGSVSWEIHRYRIFFTIL
IRESfinder result
IRESfinder score
0.754061471
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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